Lab Meeting stuff January 2012
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Jan 4
********
Bishop could not make it b/c suddenlink install
Rajib/Kim/John worked on map of all positioned nucleosome sequences



Jan 11
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updates:
1) lots of computer time: LONI + XSED ~ 10,000 SU
so focus on honing the workflow: all of the following needs to be "proofed" and integrated into easy workflow
	-making nucleosomes
	-running simulations
	-analyzing simulations
		-remove water
		-clean up/merge trajectory
		-extract/analyze helical parameters
		-energy analysis
		-pro-dna contacts
	-someone needs to test "globus online" 

2) Feb 6: bishop to CSU for fescue
	need color map as per Jan 4 of the 16 nucleosome sequences
	need information on what these 16 sequences are so Kim/John blast  each of them to find
		a) whats there
		b) compare to categories in Pugh's publication and/or Pugh's data set
	
3) Little Fe unit: 
	-put on top of other server
	-run w/ Bootable CD
	-install ROCKS on it... this is what our new 764core dell cluster will have so some experience will go  a LONG ways!
	-install NAMD  www.ks.uiuc.edu  and then check in w/ me on interactive MD


4) new workstations
	-should arrive soon
	-will make room in Data/Viz lab for Bishop/Mukerjee's old computers
		
5) need some simple programming assistance... helical parm read/manipulation/write fortran/ c or c++ 
	any takers? I can explain



Jan 18
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Jacob: little fe:

Kim/John

	formaating now works
	but some data missing

	

	biological information
		blast
		categorize them pugh data
			locaiton of of nucleosome in this sequence
			"type of sequence"
			coordinates in yeast database scgdb
		OR directly from yeast genome prject


Ian:
	eclipse
	http://www.eclipse.org/
	does this work
	Eclipse IDE for C/C++ Linux Developers (includes Incubating 



Rajib
	do a norm calc for each helical parmeter to determine "partitioning"
	do the LHS/RHS ratio calc for the eigenvector matrices
		to measure asymmetry	
		since each vector is normalized can just plot Vrhs b/c Vlhs = 1- Vrhs
			the range for Vrhs is 0 to 1
	do this mod 12 to analyze each component 
		for each component normalize the lhs or rhs by the total magnitude
			e.g. plot  Vlhs_shear/Vtot_shear
			the value for Vlhs_shear/Vtot_shear is 0 to 1
			
		lose the relative contrib from each helical parameter

	do this for artifical and actual 601 and 5srdna sequences